don't stip eol at end of file. This is bad windows behaviour

A drawback of the former solution was, that autodetection of DOS-Files was switched off. This was due to the usage of "set binary". This option also disables a lot of other vim features, btw.
If you really need to preserve "noeol" you can use PreserveNoEOL (http://www.vim.org/scripts/script.php?script_id=4550 ) in combination with an additional windows only vimrc:

Add the followin to $HOME/.vimrc_windows

:let g:PreserveNoEOL = 1
source $HOME/.vimrc

adn add the following to $HOME/extra

export VIMINIT="source $HOME/.vimrc_windows"